Revision as of 15:52, 1 August 2016

Contents

Prime: post-refinement and merging

With the latest update, prime can be used to process data on multiple nodes (on queuing system). At the moment, only LSF (bsub) is supported. See documentation below for more information how to use the queuing system.

This major update replaces prime.postrefine with

prime.run

For auto mode, you can still use prime.run with your parameter phil file like before. For manual mode, the available sub commands in prime are:

prime.genref #generates a reference set from given integration results
prime.postrefine #refines all images
prime.merge #merges all refined results for an mtz file

You can choose to run these commands independently (ideally in the above order) using the same phil file. See "PRIME flowchart". This will you a freedom to change something (e.g. set of parameters to refine, resolution cut-off, etc.) at different stages of the post-refinement and merging. See running prime in manual mode for more detail.

Step-by-step guidelines to post-refine and merge XFEL diffraction images. For more detail and citation, see
"Enabling X-ray Free Electron Laser Crystallography for Challenging Biological Systems from a Limited Number of Crystals"
"DOI: http://dx.doi.org/10.7554/eLife.05421"

NEW! PRIME IS GUIED

Thanks to Dr. Lyubimov, PRIME is also available as a Graphic User Interface program. Try it by running

Getting Started

Generating input phil file
Like most programs developed under cctbx framework, prime reads in input .phil file, which stores all the parameters needed to run post-refinement and merging steps. To generate the template .phil file, do the dry run by calling

You can save the content of the output to any file name - in this tutorial, let's save it to thermolysin.phil.

First look at your phil file
To run prime, set the required parameters to match with your experiments (you can leave other parameters with their default values - or just delete them from you .phil file). The most interesting parameters are shown below:

You should pay attention to d_min and d_max for the refinement and merging parameters. If you use IOTA to integrate the images, IOTA will output .phil file for prime that has the optimal resolution range. If not, a few trial-and-error runs may be required to get the best resolution range for your dataset. Use merging statistics output by prime and check the values of CC1/2 and I/sigI to find out your optimal resolution range.

Cell parameters (target_unit_cell and target_space_group) are required to run prime. Target cell parameter is used to remove some outlier images by controlling uc_tolerance parameter (the default value of tolerate range is 3% different). Space group parameter is used in removing outliers and merging with the given symmetry.

Don't forget also to change your pixel size in millimeters. Check what your detector is and note down its pixel size.

Running post-refinement in automatic mode
Once you have the input .phil file, you can run prime by calling

prime.run thermolysin.phil

Prime will post-refine and merge for reflection sets using three (default value) macrocycles. At the end of the run, you can obtain merging statistics in the last cycle - all other cycle statistics are also available in log.txt.